D4Potential

class D4Potential(file=None, fileD3=None, S6=None, a1=None, S8=None, a2=None, r_cut=None, bond_rcut=None, triple_rcut=None, taper_factor=None, ATM=None, EEQ_rcut=None, DSF_alpha=None, EEQ_only=None)

Constructor of the potential.

Parameters:

  • file (str) – The name of the file that contains the D4 parameters.

  • fileD3 (str) – The name of the file that contains the involved D3 parameters.

  • S6 (float) – The dimensionless BJ/Z parameter S6

  • a1 (float) – The dimensionless BJ parameter a1 By setting S6r = 0 and a1!=0 or a2!=0 one chooses BJ damping

  • S8 (float) – The dimensionless BJ/Z parameter S8

  • a2 (PhysicalQuantity of type length) – The BJ parameter a2 By setting S6r = 0 and a1!=0 or a2!=0 one chooses BJ damping

  • r_cut (PhysicalQuantity of type length) – The cutoff radius for the interactions

  • bond_rcut (PhysicalQuantity of type length) – The cutoff radius for the coordination numbers

  • triple_rcut (PhysicalQuantity of type length) – The cutoff radius for the ATM interaction

  • taper_factor (float) – The dimensionless taper_factor for bond_rcut and r_cut

  • ATM (bool) – The parameter to switch on the Axilrod-Teller-Muto three-body terms

  • EEQ_rcut (PhysicalQuantity of type length) – The cutoff radius for the EEQ interactions

  • DSF_alpha (PhysicalQuantity of type length**-1) – Damping parameter in the DSF method. It determines how fast the Coulomb interactions decay with the particle distance. For alpha >0 the DSF approach is used to approximate erf(g r)/r If alpha <= 0, it’s just erf(g r)/r

  • EEQ_only (bool) – The parameter to switch if just the EEQ term is applied (and not the C6 Dispersion term)

classmethod getAllParameterNames()

Return the names of all used parameters as a list.

getAllParameters()

Return all parameters of this potential and their current values as a <parameterName / parameterValue> dictionary.

static getDefaults()

Get the default parameters of this potential and return them in form of a dictionary of <parameter name, default value> key-value pairs.

getParameter(parameterName)

Get the current value of the parameter parameterName.

setParameter(parameterName, value)

Set the parameter parameterName to the given value.

Parameters:

  • parameterName (str) – The name of the parameter that will be modified.

  • value – The new value that will be assigned to the parameter parameterName.

Usage Examples

Define a D4 potential ([1], [2], [3]) for a Si/SiO2 interface to be used with an MTPPotential by adding particle types and interaction functions to the TremoloXPotentialSet.

# -*- coding: utf-8 -*-
# Set up lattice
vector_a = [5.4306, 0.0, 0.0]*Angstrom
vector_b = [4.440892098500626e-16, 5.4306, 0.0]*Angstrom
vector_c = [0.0, 0.0, 21.495928431319584]*Angstrom
lattice = UnitCell(vector_a, vector_b, vector_c)

# Define elements
elements = [Silicon, Silicon, Silicon, Silicon, Silicon, Silicon, Silicon,
            Silicon, Silicon, Silicon, Silicon, Silicon, Oxygen, Oxygen,
            Oxygen, Silicon, Oxygen, Oxygen, Oxygen, Silicon]

# Define coordinates
fractional_coordinates = [[ 0.17467925    ,  0.135152125   ,  0.235604166294],
                          [ 0.67467925    ,  0.635152125   ,  0.235604166294],
                          [ 0.92467925    ,  0.385152125   ,  0.298762638576],
                          [ 0.42467925    ,  0.885152125   ,  0.298762638576],
                          [ 0.67467925    ,  0.135152125   ,  0.361921110858],
                          [ 0.17467925    ,  0.635152125   ,  0.361921110858],
                          [ 0.42467925    ,  0.385152125   ,  0.42507958314 ],
                          [ 0.92467925    ,  0.885152125   ,  0.42507958314 ],
                          [ 0.17467925    ,  0.135152125   ,  0.488238055421],
                          [ 0.67467925    ,  0.635152125   ,  0.488238055421],
                          [ 0.05955       ,  0.614847875   ,  0.566340611359],
                          [ 0.392883333333,  0.114847875   ,  0.578342757834],
                          [ 0.273783      ,  0.819847875   ,  0.589473461329],
                          [ 0.845317      ,  0.599947875   ,  0.618508356925],
                          [ 0.511983      ,  0.220197875   ,  0.642334400174],
                          [ 0.726216666667,  0.410297875   ,  0.67136929577 ],
                          [ 0.94045       ,  0.220197875   ,  0.700404191366],
                          [ 0.607117      ,  0.599947875   ,  0.724230234614],
                          [ 0.17865       ,  0.819847875   ,  0.75326513021 ],
                          [ 0.05955       ,  0.114847875   ,  0.764395833706]]

# Set up configuration
bulk_configuration = BulkConfiguration(
    bravais_lattice=lattice,
    elements=elements,
    fractional_coordinates=fractional_coordinates
    )

# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------

# Create a new MTP potential set
mtp_potential_set = TremoloXPotentialSet('MTP')
mtp_potential_set.addParticleType(ParticleType('Si'))
mtp_potential_set.addParticleType(ParticleType('O'))

mtp_potential_set.addPotential(MTPPotential(
    file = 'MTP_Si_SiO2_interface_small.mtp',
    suppress_intercept = False,
))

# Create a new D4 potential set
d4_potential_set = TremoloXPotentialSet('D4')
d4_potential_set.addParticleType(ParticleType('Si'))
d4_potential_set.addParticleType(ParticleType('O'))
# D4BJ parameters for PBE.
d4_potential_set.addPotential(D4Potential(
    file=None,
    S6=+1.00000000,
    S8=+0.95948085,
    a1=+0.38574991,
    a2=+4.80688534*Bohr,
    EEQ_only=True
))

calculator = TremoloXCalculator(
    parameters=[mtp_potential_set, d4_potential_set]
)

bulk_configuration.setCalculator(calculator)

Notes

Currently only the electronegativity equilibrium model (EEQ) part of the D4 potential is available as a standalone model, which means it can only be used with EEQ_only=True.